[gmx-users] density tip3p

[Sander Pronk]

Hi Nisha,

Looking at your .mdp, there are some issues that might lead to the behavior that you describe:
First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. 
Second: your neighbor list cut-off (rlist) might be too small to fully contain the charge groups (check the manual, section 7.3.11).
Third: You haven't enabled long-range mean field correction for the pressure or energy. Expect the pressure to be strongly dependent on cut-off (see the same section).

Sander


On Mar 30, 2010, at 22:47 , nishap.patel at utoronto.ca wrote:

> I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the density decrease after the run? these are the parameters that I used :
> 
> RUN CONTROL PARAMETERS
> integrator               = md
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 50000
> nstcomm                  = 0
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> nstlog                   = 100
> nstenergy                = 100
> nstxtcout                = 0
> xtc_precision            = 1000
> nstlist                  = 5
> ns-type                  = Grid
> pbc                      = xyz
> rlist                    = 1.1
> coulombtype              = pme
> rcoulomb                 = 1.1
> epsilon-r                = 1
> vdw-type                 = switch
> rvdw-switch              = 0.8
> rvdw                     = 1.0
> Tcoupl                   = V-rescale
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300
> Pcoupl                   = berendsen
> tau_p                    = 0.5
> compressibility          = 4e-05
> ref_p                    = 1.0
> constraints              = all-bonds
> constraint-algorithm     = Lincs
> unconstrained-start      = no
> lincs-order              = 4
> lincs-iter               = 1
> lincs-warnangle          = 30
> 
> Am I missing something?
> Thanks
> 
> Nisha Patel
> 
> 
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